A lot of unix apps store your preferences in an invisible file in your home directory. For example, GPG stores your keyrings and information in an invisible directory named .gnupg. Backup totally ignores these files, which can be disastrous if you're not manually backing up these files. You can, however, force Backup to include these files.

First, find out what invisible files there are by going to the Terminal, navigating to your home directory if necessary (it shouldn't be), and then typing ls -laF. This will give you a directory listing that includes the invisible files and directories.

Now, open Backup and select File -> Add... When the open sheet comes up, the invisible files will be, well, invisible. Now, simply type tilde (~) which represents your home directory, slash, then the name of the invisible file. For example, to add the previously mentioned .gnupg directory, type ~/.gnupg and press the Choose button. The invisible file or folder is now added to your backup items and can be turned on or off like any others.

Hi all- just thought I'd offer a little background on these invisible files/directories. Back in MacOS 9 days, an invisible file was one that had a metadata attribute set on it (i.e., a thing that was not part of the name, or part of the contents of the file) that told the Finder (and the standard file services dialogs, etc) not to display the file when somebody asks. This was an attribute that a file could have in HFS and HFS+. To my knowledge, this attribute is still around today, although I don't know if the OS X Finder honors it or not.

The Invisible files that are mentioned in this hint are invisible as a hold-over from a convenience feature of unix shells, and the 'ls' program. Almost all unix programs that require any settings store their settings in files that are called "dot files" or "resource files" or "rc files". The first term stems from the fact that they all begin with a ".". The other two from the fact that the files store resources that the program will use, and commonly the file names will end in the letters "rc". (Note that this has nothing to do with a Mac resource fork.) Anyway, since so many programs would create these dot files, and most of the time you want to ignore them, it was a pretty good idea simply not to show any file that began with a "." unless they were specifically asked for.

Because there are still enough unix-isms in MacOS X, Apple wisely expected that users would start accumulating dot files and chose to have the finder/file services hide those as a convenience. And that's your unix culture lecture of the day.